Genome-wide analysis of the NLR gene family in strawberry reveals a novel immune receptor architecture in Rosaceae

Background: Nucleotide-binding leucine-rich-repeat receptors (NLRs) are key components of plant innate immunity. These intracellular proteins specifically recognize pathogen effectors and subsequently activate a defense response. The genes encoding these proteins comprise one of the largest and most diverse gene families in plants. Understanding the various forms and functions of these proteins is imperative to the goal of generating disease resistant crops. This is particularly important for cultivated strawberry, which is heavily impacted by disease. Results: Using conserved motifs and functional domains, we identified 823 NLR-encoding genes (NLRs) in the ( Fragaria \((\times)\) ananassa ) `FaRR1' genome and categorized them according to their association with the anciently diverged RNL, CNL, and TNL classes. Among these, 45 were newly annotated and 149 were predicted to be full-length. 94 genes exhibited a previously unreported architecture, containing both CNL-specific and TNL-specific sequences. This architecture was supported by full-length transcript data and was found to be present in additional Rosaceous species but not in any non-Rosaceous species examined. Expression analyses revealed that 583 NLRs, including nearly all those with the novel mixed architecture, were differentially expressed following inoculation with at least one of five pathogens. Conclusions: Our genome-wide analysis expands the catalog of NLR genes in cultivated strawberry and uncovers a previously undescribed form of domain organization that appears to be unique to the Rosaceae family. The results suggest that recombination or domain swapping among N-terminal regions has contributed to NLR diversification in this lineage, providing insight into the evolutionary and functional basis of pathogen recognition in strawberry.